February 2011 - galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] Quality Score
by Peter Cock 28 Feb '11

28 Feb '11

Great :) Don't forget to CC the mailing list in future ;) On Fri, Feb 25, 2011 at 4:46 PM, Amy Boddy <aboddy(a)med.wayne.edu> wrote: > Thank you, these articles helped! > > On Thu, Feb 24, 2011 at 5:47 PM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: >> >> On Thu, Feb 24, 2011 at 8:47 PM, Amy Boddy <aboddy(a)med.wayne.edu> wrote: >> > Hello, >> > I was wondering how Galaxy calculates the quality score for NGS data? >> > Is there any documentation I could read on how this is calculated? >> > Thanks! >> > -Amy Boddy >> >> Which quality score are you talking about? Raw reads? Mappings? >> If it's FASTQ files you mean, may I suggest: >> >> http://dx.doi.org/10.1093/nar/gkp1137 >> >> and >> >> http://en.wikipedia.org/wiki/FASTQ_format >> >> Peter > > > > -- > Amy Boddy > Ph.D Candidate > Center for Molecular Medicine & Genetics > Wayne State University School of Medicine > 540 E. Canfield, Detroit MI 48201 > Website: http://homopan.wayne.edu/ > Phone: 313.577.0086 > email: aboddy(a)med.wayne.edu > > >

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de-novo motif analysis
by Christopher Futtner 25 Feb '11

25 Feb '11

Two questions - 1. When I call peaks with MACS on Galaxy I get different results than if I run MACS on my machine via command line. I'm using default parameters in both instances. 2. Are there any tools in galaxy for doing de-novo motif analysis of the peaks that I have called. If not can anyone suggest their favorite programs for doing so? I prefer a web interface but can fumble my way around using command line. Thanks, Chris Christopher Futtner Duke University, Onaitis Lab 919-684-1183 106 Research Dr. MSRB II, rm. 2045 Bay 11 Durham, NC. 27710

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de-novo motif analysis
by Christopher Futtner 25 Feb '11

25 Feb '11

Two questions - 1. When I call peaks with MACS on Galaxy I get different results than if I run MACS on my machine via command line. I'm using default parameters in both instances. 2. Are there any tools in galaxy for doing de-novo motif analysis of the peaks that I have called. If not can anyone suggest their favorite programs for doing so? I prefer a web interface but can fumble my way around using command line. Thanks, Chris -- Christopher Futtner Onaitis Lab / Duke University 919-684-1183 106 Research Dr. MSRB II rm 2045 Durham, NC. 27710

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FASTA Generation from Pileup for SNP Detection
by John David Osborne 25 Feb '11

25 Feb '11

I'm interested in generating a fasta file from Ilumina paired reads of my wild type strain. I have an NCBI reference genome I can assemble against and I have already uploaded my 2 reads (using the NCBI reference as my genome), used fastq groomer, aligned them with bowtie and generated my pileup. What I think I want to do though is to extract from the pileup a consensus fasta file (using 20 or something as a quality cutoff threshold) and then used that as my new reference genome to align 2 mutant strains against that are from that genetic background. How can I do that in Galaxy? I don't see any way to go from pileup to fastaq or pileup to fasta using some sort of cutoff. I think I can use samtools pileup2fq based on web posts (and then used something else to make a fasta file), but I would like to do all my analysis in galaxy. Is this possible? Any help appreciated, I am new with Galaxy. -John

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Quality Score
by Amy Boddy 24 Feb '11

24 Feb '11

Hello, I was wondering how Galaxy calculates the quality score for NGS data? Is there any documentation I could read on how this is calculated? Thanks! -Amy Boddy -- Amy Boddy Ph.D Candidate Center for Molecular Medicine & Genetics Wayne State University School of Medicine 540 E. Canfield, Detroit MI 48201 Website: http://homopan.wayne.edu/ Phone: 313.577.0086 email: aboddy(a)med.wayne.edu

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Groomer
by Johnson, Kory (NIH/NINDS) [C] 24 Feb '11

24 Feb '11

Hello, Do you have a chart or table that projects time for Groomer to complete vs number of reads provided? Have submitted job totaling 25M Illumina reads in FASTQ v1.3+ format and it is taking time on the order of days. What would be helpful, if not on the development schedule is a progress bar or % completed reported as text, anything to give indication that the job submitted is processing correctly, not hung, and it can be estimated how long it will take. Thank you, Kory Johnson -------------------------------------------- Kory R. Johnson, MS, PhD Sr. Bioinformatics Scientist [cid:image001.jpg@01CBD41D.D48D9620] www.kellygovernmentsolutions.com Providing Contract Services For: Bioinformatics Section, Information Technology & Bioinformatics Program, Division of Intramural Research (DIR), National Institute of Neurological Disorders & Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland Mailing Address: NINDS/NIH Clinical Center (Building 10) Office 5S223 9000 Rockville Pike Bethesda, MD 20892 Contact Information: Phone: 301-402-1956 Fax: 301-480-3563 email: johnsonko(a)ninds.nih.gov P Green Message: Please consider the environment before printing this e-mail. Thank you. Important Message: This electronic message transmission contains information intended for the recipient only. Such that, the information contained herein may be confidential, privaledged, or proprietary. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of this information is strictly prohibited. If you have received this electronic information in error, please notify the sender immediately by telephone. Thank you. --------------------------------------------

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Replicates
by Motallebipour, Mehdi 24 Feb '11

24 Feb '11

Hi, I am trying to analyze some RNA-seq data using the Galaxy. The reads for each sample comes from 3 lanes, so I need to integrate these three lane reads to be able to make a comparison between my samples. How do I 'put together' these three read-files? Is there any tools available in Galaxy for that, which I have missed? Unfortunately I do not have any programming skills. Many thanks, Mehdi M ---------------------------------------- Mehdi Motallebipour, PhD Mammalian Neurogenesis MRC Clinical Sciences Centre Imperial College London Hammersmith Hospital Campus Du Cane Road London W12 0NN United Kingdom Tel: +44-20-8383 8285

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FTP access to Galaxy data?
by Ready, Robert F Jr 24 Feb '11

24 Feb '11

Greetings, I am wondering if there is a way to directly access data sets created and stored on Galaxy. A >50Gb set of raw sequencing results was uploaded via FTP, and is currently being groomed and clipped. Following the clipping, we would like to download a copy to a local cluster for analysis with tools not available on Galaxy. The only way I can find to do this is to download via the web interface to a local computer, then copy the data to the cluster. I'd rather not move the data twice if I can help it. Is there a way that I can access Galaxy datasets via the command line on our cluster, perhaps making the data available via FTP, so that I can directly download it to the place it needs to be? Thank you, Bob ------------------------------------------ Robert Ready Undergraduate Research Assistant Logsdon Lab Department of Biology University of Iowa

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Map with Bowtie for Illumina
by Sonali Thakur 23 Feb '11

23 Feb '11

Hello, We are getting below error with the Map with Bowtie for Illumina<http://rave.cshl.edu/galaxy/tool_runner?tool_id=bowtie_wrapper>tool. Please suggest. Traceback (most recent call last): File "/var/www/galaxy/lib/galaxy/jobs/runners/local.py", line 55, in run_job job_wrapper.prepare() File "/var/www/galaxy/lib/galaxy/jobs/__init__.py", line 347, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/var/www/galaxy/lib/galaxy/tools/__init__.py", line 1515, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/var/www/galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/var/www/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 222, in respond IndexError: list index out of range Thanks

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GeneTrack Server Error
by Felix Hammer 23 Feb '11

23 Feb '11

Hi, I am trying to view Converted Interval Data in GeneTrack, but all I get is "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" thx, Felix

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